Jumper bay
From SGCommand
The Jumper bay, which is located on top of the central tower of Atlantis, houses the small ships. The room is a large two-floor room which can store the Jumpers on the floor or on platforms on the upper area. The upper area also contains a gangway which runs on the walls and provides access to the platforms. The room provides two possibilities for the Jumpers to leave it: the first is a large panel in the middle of the floor which leads directly to the large platform of the gate room, so that the Jumper can fly immediately through the Stargate. The second possibility is another panel that is located in a small shaft in the ceiling and thus allows the Jumper to leave the city to fly to other locations on the planet or star system. This panel was however discovered later.
While the Asurans controlled Atlantis, Sheppard flew a Puddle jumper into the control room and dropped a payload. The explosive detonated and destroyed the control room and a good part of the tower. It presumably destroyed the jumper bay as well. later, the Jumper bay was seen intact and its design was different from the first one: It was a much larger room and was not in a perfect circle, meaning that when the Asurans rebuilt the Jumper bay, they may have changed the design.
Atlantis also has at least one jumper bay on its underside specifically designed for underwater entry and egress. The control station is dedicated to pressurization and pumping systems for the underwater bay. However, the bay itself has not been used in some time and automated jumper controls did not activate any pressurization mechanisms as expected. The bay's doors have also since been jammed shut after being used by Colonel Sheppard's team to infiltrate the city.
